MER4D1
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000803 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Haplorrhini |
| Length | 900 |
| Kimura value | 12.09 |
| Tau index | 0.9731 |
| Description | MER4D1 Long Terminal Repeat for ERV1 endogenous retrovirus |
| Comment | MER4D1 LTR is a ~90% identical variant of MER4D, which itself is a ~192 bp insertion variant with respect to MER4B. Note that MER stands for MEdium Reiteration frequency interspersed repeat. As such, MERs as a group are a grab bag of DNA transposons and retrotransposons. |
| Sequence |
TGTAAACCAAAAATAAAATTCTAAGCCCCCCAACCGACTGAATGGACCCCTCCTCTCGGCCAAGGGCATTCCAAAGTAAACCTGAAAAACTAGTTCAGGCCATGATGGGAAGGGGGGGTCGGACATGCCTCATTATACCCTCCTCCCTTTGGAATTCAGGCACAACTGACCAGCATTAACATTAAAACAGAGATCTTAAGACTGACAAAACAGACTCTTTGTAGCAATAAGATACCAAATTCCAACCTGACTCTAGTATAGCATCACATGACAGATAGCAGGCCCTGAAAGAAATCGAAGTATTTTACCCCAAAATATATTTCTTTGACATATTTTGAAATGGCCCTGCAAAGCTGTCTCTTGTGGGGAAAATCTACATTCTGTAGAGAATCCCCTTCCCTTTCCAGGTCTTTTTCCTGATCCAGGAGAGAATTAACTAAGAGTCTGGCACCTTTTTAAGTCTGATAAGAAACATTTACAATCTATTCTCTCTGAAGCCTGCTACCTGGAGGCTTCATCTGCATGATAAGAACCTTGGTCTCCACAACCCCTTATCTTAACCCAGACACTCCTTTCTATTGATTCCAGGTCTTTAGATAATAACTNAACTCTTTCAACCAATTGCCAATCAGAAAATCTTTGAATCCACCGTATGACCTGGAAGCCCCCCCCTCCACTTCGAGTTGTCCCGCCTTTCCGGACCGAACCAATGTACATCTTACATGTATTGATTGATGTCTTATGTCTCCCTAAAATGTATAAAACCAAGCTGTAGCCCGACCACCTTGGGCACATGTTCTCAGGATCTCCTGGGGCTGTGTCACGGGCCATGGTCACTCATATTTGGCTCAGAATAAATCTCTTCAAATATTTTACAGAGTTTGACTCTTTTCGTCGACA
|
TF motifs of the concenus sequence
Use FIMO to detect transcription factor motifs in the concenus sequence of the TE family.
| TE_family | TFBS | Start | End | Strand | Score | Matched sequence |
|---|---|---|---|---|---|---|
| MER4D1 | AT4G12670 | 7 | 35 | + | -15.49 | CCAAAAATAAAATTCTAAGCCCCCCAACC |
| MER4D1 | EWSR1-FLI1 | 134 | 151 | - | -15.92 | CAAAGGGAGGAGGGTATA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
